Optimization of an RNA-centric approach searching for RNA-interacting proteins in Arabidopsis thaliana

ABSTRACT: The number of methods used to study RNA-protein interactions in plants is currently relatively limited. The RNA-centric approach, starting with RNA of interest, brings several difficulties, especially when the RNA belongs to the less abundant RNAs. These methods for identification of RNA-interacting proteins used to be developed for different model systems, however, their application in plants is delayed. The Comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS) method was originally developed for mammalian cells. This work describes the modified ChIRP-MS procedure applicable in Arabidopsis thaliana. All steps were optimized for the telomerase RNA which was recently described as a low-abundant RNA. Following this optimization procedure, it is possible to use ChIRP-MS as a screening method for the identification of candidate proteins interacting with the target RNA.

INSTRUMENT(S):

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Whole Body

SUBMITTER: Katerina Hanakova  

LAB HEAD: Zbynek Zdrahal

PROVIDER: PXD046839 | Pride | 2024-05-22

REPOSITORIES: Pride